Baked Pumpkin Mac and Cheese
This Baked Pumpkin Mac and Cheese is a holiday favorite, loved by all. It’s simple to prepare, with lots of cheese of course, then baked to perfection. Your holiday table will never be the same!

Do you know of anyone who hates macaroni and cheese? I sure don’t! While people have their own preferences… stovetop or baked, creamy or custardy… I like them all! Baked mac and cheese comes with that layer of crispy cheese on top which can’t be overlooked!
This pumpkin mac and cheese can be enjoyed year round, but it’s particularly festive for Halloween, Thanksgiving, Friendsgiving, or any autumnal gathering!
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Why this recipe works
- Easy and Forgiving to Make: This recipe is beginner-friendly with no complicated techniques. Even if you’re not precise with measurements, it still turns out delicious. No fancy equipment or hard-to-find ingredients required.
- Make-Ahead Friendly: Perfect for busy holiday schedules, this dish can be prepared in advance and baked right before serving. It reheats beautifully, too!
- A Crowd-Pleaser: Everyone who tries it falls in love! The combination of gooey cheese and subtle pumpkin makes this holiday twist on a classic recipe a hit with kids and adults alike.
- Comforting and Indulgent, Yet Balanced: This dish is rich and satisfying without being overly heavy. There’s no cream, and the pumpkin adds a great flavor while also packing in fiber and nutrients. And that layer of baked cheese on top can’t be beat!
Ingredients

- Pasta: Macaroni, cavatappi, fusilli, or any shape with ridges and crevices work best to soak up the sauce.
- Butter: Forms the foundation of the roux, adding richness and a smooth, velvety texture to the sauce.
- Optional Aromatics: You can add sage leaves, chopped shallots, or minced garlic to the butter to enhance the overall flavor if you want!
- All-Purpose Flour: A key thickener in the roux, ensuring the sauce clings to the pasta with the perfect consistency.
- Milk: Adds creaminess and helps balance the flavors in the sauce. Opt for whole milk for the richest result.
- Seasonings: Salt of course. We add paprika, garlic powder, and onion powder for extra flavor, and pumpkin pie spice to enhance the pumpkin flavor.
- Pumpkin Purée: Infuses the sauce with a velvety texture, orange color, and mild sweetness, while also (unintentionally) adding a nutritional boost.
- Cheeses: The heart of macaroni and cheese! Here we use three cheeses: sharp cheddar for tang, colby jack for silkiness, and gruyere for a nutty depth.
See recipe card for quantities.
Instructions for Baked Pumpkin Mac and Cheese
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- Prepare: Preheat oven to 350 degrees F and grease a 3 qt baking dish (9×13″). Boil the pasta al dente, drain, and set aside.
- Shred the cheese: While water is coming up to a boil, shred cheeses and toss together to mix. Separate out ⅓ of the shredded cheese to save for topping, leaving about ⅔ of the shredded cheese intended for mixing into the sauce.
- Make the sauce: Melt butter in a large pot over medium heat. Sprinkle in flour and whisk to combine. Cook for 1-2 minutes, whisking every so often. Slowly pour in the milk and spices while whisking, until combined and smooth. Pour in the pumpkin puree and whisk until combined.
- Add the cheese: Remove from the heat and, using a spatula, stir in the shredded cheese intended for the sauce. It’s okay if you still see some small chunks of cheese – this will create pockets of gooeyness in the end result.
- Combine and bake: Add the cooked pasta to the pot with the cheese sauce. Pour the pasta mixture into the prepared baking dish, then top with the remaining shredded cheese. Bake for 30 minutes or until the cheese has melted and becomes bubbly. Option to leave under the broiler for the last minute. Serve and enjoy!

Substitutions and Variations
- Cheeses – I love the combination of sharp cheddar, colby jack, and gruyere for this pumpkin mac and cheese recipe. However, you can swap these for other cheeses such as mozzarella instead of colby jack, adding moterey jack, gouda instead of gruyere, or adding parmesan. As long as the total amount of cheese remains the same.
- Aromatics – You can sautee diced shallots or garlic into the butter while adding the roux for some depth of flavor. You can also toast fresh sage leaves as well. If you do, be sure to remove the sage leaves before adding the flour, and you can add them back at the very end on top of the final cheese layer.
- Spices – Feel free to mix up the spices depending on your preferences. Add some red pepper flakes for some spice, or some mustard for depth.

Storing Baked Pumpkin Mac and Cheese
You can prep the pre-baked pumpkin mac and cheese one day ahead, then pop into the oven straight from the fridge.
Once the pumpkin macaroni and cheese has been baked, you can store in the fridge for up to five days. Reheat in the oven or microwave. You may want to add a bit of butter or milk when reheating as it could dry up over time.
Top Tip
Shred your own cheese! There is a huge textural difference when you shred cheese from a block, as opposed to buying pre-shredded cheese. You can use a box grater, but if you have a food processor with the shredding attachment, it will be much less work!
Other recipes
- Butternut Squash and Spinach Lasagna Rollups
- Moster Mac and Cheese
- Crispy Caramel Chocolate Chip Cookies
Rate this Baked Pumpkin Mac and Cheese Recipe
If you make this Baked Pumpkin Macaroni and Cheese recipe, be sure to give this recipe a rating and/or leave a comment! It means the world to hear from you. Also, don’t forget to tag me on Instagram or TikTok @snackingemily so I can see what you’re making! I love to see your creations!

Baked Pumpkin Mac and Cheese
Ingredients
Baked Pumpkin Mac and Cheese
- 1 lb short-form pasta such as macaroni, fusilli, or cavatappi
- ¼ cup butter
- ¼ cup all-purpose flour
- 2 cups milk add ½ cup more for a more creamy sauce.
- ½ teaspoon kosher salt
- ½ teaspoon paprika
- ½ teaspoon pumpkin spice
- ½ teaspoon garlic powder
- ½ teaspoon onion powder
- 1 cup pumpkin puree
- 16 oz sharp cheddar cheese
- 16 oz colby jack cheese
- 6 oz gruyere cheese
Optional Aromatics
- 10 fresh sage leaves
- 1 shallot diced
- 3 cloves garlic diced
Instructions
- Preheat oven to 350 degrees F and grease a 3 qt baking dish (9×13″). Set aside.
- Boil the pasta according to package instructions in heavily salted water. Cook for 1-2 minutes less than instructed. Drain and set aside, tossing once after a few minutes to avoid the noodles sticking together. Do not rinse.
- While water is coming up to a boil, shred cheeses and toss together to mix, then separate out ⅓ of the shredded cheese to save for topping, leaving about ⅔ of the shredded cheese intended for mixing into the sauce.
- Melt butter in a large pot over medium heat. Option to add aromatics here (see Note 1 for instructions if doing so). Once melted, sprinkle in flour and whisk to combine. Mixture will look like very wet sand. Cook for 1-2 minutes, whisking every so often. Slowly pour in about 1 cup of the milk, while whisking constantly, until smooth. Add the spices and whisk to combine. Slowly pour in the remaining milk, while whisking, until combined and smooth.
- Pour in the pumpkin puree and whisk until combined. Continue to cook for about 1 minute.
- Remove from the heat and, using a spatula, stir in about half of the cheese intended for mixing into the sauce. Mix until combined, then add the remainder of the cheese intended for the sauce. It’s okay if you still see some small chunks of cheese – this will create pockets of gooeyness in the end result.
- Add the cooked pasta to the pot with the cheese sauce. Stir to combine fully, about 1-2 minutes.
- Pour the pasta mixture into the prepared baking dish, then top with the remaining shredded cheese.
- Bake for 30 minutes or until the cheese has melted and becomes bubbly. Option to leave under the broiler for the last minute. Serve and enjoy!



